workspace\(catalogs\)referencePanels

Reference Panel Catalog

Description

Inventory and management utility for workspace reference panel resources.

Details

Inventory and management utility for reference panels used by PolyGenius.

Use this catalog through workspace$catalogs$referencePanels.

Behavior

  • Exposes the union of downloadable manifest entries and local cache entries.

  • Treats the manifest as read-only.

  • add() and remove() operate only on local cache resources.

Main methods

  • view(): inventory rows with local/downloadable availability.

  • get(name, build, format = NULL): build a ResourceSpec for retrieval.

  • add(…) / remove(…): manage only local cached entries.

Methods

Public methods

Method new()

Initialize reference panel catalog.

Usage 
ReferencePanels$new(manifest.path = NULL)
Arguments
manifest.path

Optional custom manifest CSV path.

Method view()

View the union inventory of local and downloadable panels.

Usage 
ReferencePanels$view()
Returns

data.frame inventory with availability flags.

Method get()

Build a ResourceSpec for a requested reference panel, optionally executing resolution immediately.

Usage 
ReferencePanels$get(
  name,
  build = NULL,
  format = NULL,
  variant.space = NULL,
  .execute = TRUE,
  .status = polygenius.option.execution.status()
)
Arguments
name

Panel name.

build

Optional genome build key/name filter.

format

Optional panel format filter.

variant.space

Optional variant-space name. When supplied, the catalog resolves a derived reference-panel spec restricted to that variant space. name must refer to an unrestricted reference panel.

.execute

Logical; when TRUE, trigger reactive execution to ensure the requested panel resource is available in cache.

.status

Optional execution-status mode override (“auto”, “yes”, “no”).

Returns

When .execute = TRUE, the resolved reference panel resource. When .execute = FALSE, a ResourceSpecSet.

Method add()

Add one or multiple local reference panels to the cache from GenotypeInfo objects. Split inputs are merged into one fileset and then tidied before they are persisted as cached reference panels.

Usage 
ReferencePanels$add(..., overwrite = FALSE)
Arguments
…

One or more GenotypeInfo objects. When an argument is named, that argument name is used as the panel name; otherwise the GenotypeInfo$name is used.

overwrite

Logical; overwrite existing cached panel(s) with matching name + build + format.

Returns

Invisible ResourceSpec or list of ResourceSpec.

Method remove()

Remove cached reference panels matching optional filters.

Usage 
ReferencePanels$remove(name = NULL, build = NULL, format = NULL)
Arguments
name

Optional panel name filter.

build

Optional genome build filter.

format

Optional format filter.

Returns

Invisible NULL.

Method key()

Resolve a user-facing reference-panel name or key.

Usage 
ReferencePanels$key(name)
Arguments
name

User-facing name or internal key.

Returns

Internal key.

Method assert.unrestricted()

Validate that a reference-panel name is not already restricted.

Usage 
ReferencePanels$assert.unrestricted(name)
Arguments
name

User-facing name or internal key.

Returns

Invisible TRUE.

Method print()

Print reference panel inventory summary.

Usage 
ReferencePanels$print(...)
Arguments
…

Unused.